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We study a graph partitioning problem motivated by the simulation of the physical movement of multi-body systems on an atomistic level, where the forces are calculated from a quantum mechanical description of the electrons. Several advanced…
Molecular dynamics simulations use statistical mechanics at the atomistic scale to enable both the elucidation of fundamental mechanisms and the engineering of matter for desired tasks. The behavior of molecular systems at the microscale is…
Molecular dynamics (MD) simulation is widely used to study protein conformations and dynamics. However, conventional simulation suffers from being trapped in some local energy minima that are hard to escape. Thus, most computational time is…
We describe collective-move Monte Carlo algorithms designed to approximate the overdamped dynamics of self-assembling nanoscale components equipped with strong, short-ranged and anisotropic interactions. Conventional Monte Carlo simulations…
Many parallel and distributed computing research results are obtained in simulation, using simulators that mimic real-world executions on some target system. Each such simulator is configured by picking values for parameters that define the…
Particle-based shape modeling (PSM) is a popular approach to automatically quantify shape variability in populations of anatomies. The PSM family of methods employs optimization to automatically populate a dense set of corresponding…
The introduction of Single Instruction Multiple Data (SIMD) instructions in mainstream CPUs has enabled modern database engines to leverage data parallelism by performing more computation with a single instruction, resulting in a reduced…
We introduce machine learning models of quantum mechanical observables of atoms in molecules. Instant out-of-sample predictions for proton and carbon nuclear chemical shifts, atomic core level excitations, and forces on atoms reach…
A large body of animation research focuses on optimization of movement control, either as action sequences or policy parameters. However, as closed-form expressions of the objective functions are often not available, our understanding of…
We present an efficient parallel algorithm for statistical Molecular Dynamics simulations of ion tracks in solids. The method is based on the Rare Event Enhanced Domain following Molecular Dynamics (REED-MD) algorithm, which has been…
For nearly the past 30 years, Centroid Molecular Dynamics (CMD) has proven to be a viable classical-like phase space formulation for the calculation of quantum dynamical properties. However, calculation of the centroid effective force…
Visual Molecular Dynamics (VMD) is one of the most widely used molecular graphics software in the community of theoretical simulations. So far, however, it still lacks a graphical user interface (GUI) for molecular manipulations when doing…
Molecule pretraining has quickly become the go-to schema to boost the performance of AI-based drug discovery. Naturally, molecules can be represented as 2D topological graphs or 3D geometric point clouds. Although most existing pertaining…
Decades of hardware, methodological, and algorithmic development have propelled molecular dynamics (MD) simulations to the forefront of materials-modeling techniques, bridging the gap between electronic-structure theory and continuum…
Autonomy and electrification in automotive control systems have made modern-day powertrains one of the most complex cyber-physical systems. This paper presents a benchmark algorithm to quantify the performance of complex automotive systems…
Atomistic modeling of thin-film processes provides an avenue not only for discovering key chemical mechanisms of the processes but also to extract quantitative metrics on the events and reactions taking place at the gas-surface interface.…
Optimization of beamlines and lattices is a common problem in accelerator physics, which is usually solved with semi-analytical methods and numerical optimization routines. However, these are usually of the gradient-free or…
Computation of biological processes creates great promise for everyday life and great challenges for physical scientists. Simulations of molecular dynamics appeal to biologists as a natural extension of structural biology. Once biologists…
Methods to extract information from the tracking of mobile objects/particles have broad interest in biological and physical sciences. Techniques based on simple criteria of proximity in time-consecutive snapshots are useful to identify the…
We review a family of local algorithms that permit the simulation of charged particles with purely local dynamics. Molecular dynamics formulations lead to discretizations similar to those of ``particle in cell'' methods in plasma physics.…